[gmx-users] Fatal error: Number of atoms in Topology is not the same as in Trajectory
shima_arasteh2001 at yahoo.com
Sat Jan 5 09:46:47 CET 2013
I have a system of POPC/Protein/water/ions to simulate. I am trying to simulate this system by getting ideas from Justin's tutorial of kalp15-dppc.
I've passed all steps of EM, NVT, and NPT as I expected. But when I want to run mdrun, I get some errors about waters can not be settle. So, I tried to remove them from npt.gro, update the number of atoms in .gro file, and then update number of SOL molecules in top file.Finally I made a new index file to go on.
Next, to start mdrun, I run this command:
grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -n index-new.ndx -o md_0_1.tpr
and get this fatal error:
Number of atoms in Topology is not the same as in Trajectory.
In fact, I thought of updating npt.cpt file, but it's a binary file and I guess it's impossible. Does anybody knows what should I do? Would you please give me advice?
Thanks in advance.
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